Baking two textures into one
When objects were separate, they had their own UV maps as they should have been textured. Let's assume these are called "UVmap" as by default.
Objects had their materials, I assume they were called "Material_1" and "Material_2"; let's call the new material created esspecially for the bake as "Material_Bake". 

After joining objects create new UV map and call it "UVmap_For Bake". 
Make some arrangements on that new UV map so faces not overlap there (the easiest way is to press Ctrl + P with everything selected that you'd like to rearrange while in UV/Image Editor). 

For "Material_1" and "Material_2" in Texture tab, Mapping scroll set Map option to "UVMap", so that the original images are mapped using original map.
For "Material_Bake" choose in Texture > Mapping > Map your new UV map "UVmap_For Bake" so that baked texture to be mapped on the both objects with arranged map:





It seems in your file "BakedMaterial" was assigned to all the model's faces, therefore others didn't affect on the final result.
The original materials should be assigned to those parts of mesh which they were created for. 
After joining, you create that new material, but don't assign it to anything or you'll get circular reference in texture stack, empty result, rewritten images etc. Just create it and proceed to the next steps. You can look at 2 ways of how materials were assigned below.

 

It's most likely that you won't get expected result of baking in the second case.

The file below is the one with the result of incorrect baking, slightly edited. Open it, press Bake and enjoy. It'll bake generated images of one color (unfortunately your files weren't packed) into "Texture_For_Baking" texture.